MCL coexpression mm9:734: Difference between revisions
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{{MCL_coexpression_mm9 | 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transporter activity;0.000749205781920186;170762,234865!GO:0051028;mRNA transport;0.00407034741706452;170762,234865!GO:0050658;RNA transport;0.00407034741706452;170762,234865!GO:0051236;establishment of RNA localization;0.00407034741706452;170762,234865!GO:0050657;nucleic acid transport;0.00407034741706452;170762,234865!GO:0006403;RNA localization;0.00407034741706452;170762,234865!GO:0005643;nuclear pore;0.00407034741706452;170762,234865!GO:0065002;intracellular protein transport across a membrane;0.00407034741706452;170762,234865!GO:0015931;nucleobase, nucleoside, nucleotide and nucleic acid transport;0.00407034741706452;170762,234865!GO:0046930;pore complex;0.00407034741706452;170762,234865!GO:0044453;nuclear membrane part;0.00429391984070031;170762,234865!GO:0031965;nuclear membrane;0.00429391984070031;170762,234865!GO:0044428;nuclear part;0.00746703842105303;70052,170762,234865,101943!GO:0006913;nucleocytoplasmic transport;0.00746703842105303;170762,234865!GO:0051169;nuclear transport;0.00746703842105303;170762,234865!GO:0017056;structural constituent of nuclear pore;0.00764090439970906;170762!GO:0005635;nuclear envelope;0.00886461988172955;170762,234865!GO:0005681;spliceosome;0.0143799144534344;70052,101943!GO:0046540;U4/U6 x U5 tri-snRNP complex;0.0160755416039761;70052!GO:0008380;RNA splicing;0.0197360766737931;70052,101943!GO:0051649;establishment of cellular localization;0.0243803738730018;170762,234865,109658!GO:0051641;cellular localization;0.0244002357987189;170762,234865,109658!GO:0004526;ribonuclease P activity;0.0248546207161951;67724!GO:0006397;mRNA processing;0.0248546207161951;70052,101943!GO:0006406;mRNA export from nucleus;0.0248546207161951;234865!GO:0030532;small nuclear ribonucleoprotein complex;0.0248546207161951;70052!GO:0043123;positive regulation of I-kappaB kinase/NF-kappaB cascade;0.0248546207161951;18572!GO:0004549;tRNA-specific ribonuclease activity;0.0261400419890448;67724!GO:0016071;mRNA metabolic process;0.027836696568666;70052,101943!GO:0043122;regulation of I-kappaB kinase/NF-kappaB cascade;0.0284511320653779;18572!GO:0006405;RNA export from nucleus;0.0294935597533027;234865!GO:0012505;endomembrane system;0.0328158581290779;170762,234865!GO:0016891;endoribonuclease activity, producing 5'-phosphomonoesters;0.0369009904895174;67724!GO:0032991;macromolecular complex;0.0382548377726184;70052,170762,234865,101943!GO:0016893;endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters;0.0382548377726184;67724!GO:0051168;nuclear export;0.0388742433313261;234865!GO:0006396;RNA processing;0.0398025270092647;70052,101943!GO:0031975;envelope;0.0437951567695661;170762,234865!GO:0031967;organelle envelope;0.0437951567695661;170762,234865!GO:0006886;intracellular protein transport;0.0448957993436601;170762,234865!GO:0016070;RNA metabolic process;0.0499137677017831;70052,230908,18572,101943!|ontology_enrichment_celltype=CL:0002242!1.39e-07!16|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0004177!1.06e-09!29;UBERON:0005057!1.06e-09!29;UBERON:0000153!2.15e-09!43;UBERON:0001048!2.09e-08!134;UBERON:0002370!1.70e-07!23;UBERON:0000974!1.70e-07!23;UBERON:0004807!1.70e-07!23;UBERON:0005058!1.70e-07!23;UBERON:0003351!1.70e-07!23;UBERON:0009113!1.70e-07!23;UBERON:0003295!1.70e-07!23;UBERON:0009722!1.70e-07!23;UBERON:0005562!1.70e-07!23;UBERON:0007690!1.70e-07!23;UBERON:0000065!5.02e-07!41;UBERON:0000077!6.08e-07!35;UBERON:0006562!6.25e-07!24;UBERON:0001557!6.25e-07!24;UBERON:0001042!6.25e-07!24;UBERON:0008814!6.25e-07!24;UBERON:0009145!6.25e-07!24;UBERON:0007811!7.77e-07!36;UBERON:0000072!8.81e-07!27|tfbs_overrepresentation_for_novel_motifs=0.860199,0.352573,0.807108,0.360062,0.200163,0.373426,0.458558,0.392928,0.411053,0.771958,1.071,0.447169,0.124608,2.06188,0.214197,0,1.57859,0.19356,0.113609,0.205418,0.26524,0.145076,2.05901,0.198877,0.304728,0.496413,0.107695,0.392919,0.67135,0.572447,0.989437,0.754912,0.191698,0.646834,1.1554,0.6066,0.541514,1.12869,0.166348,0.143746,0.196807,0.38461,0.307718,0.617704,0.249283,0.349801,1.41649,0.407653,0.104497,0.677281,0.639101,0.522137,0.0747297,0.894161,0.911367,1.20022,0.249055,0.435119,0.101408,0.47505,1.74318,0.531188,0.140453,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,0.281085,0.404236,0.996746,0.944464,1.09617,0.623453,0.0942164,0.567793,0.718494,0.268962,0.129727,0.673009,0.529804,0.119727,0.830765,0.318393,0.0149522,0.271714,1.42647,1.55487,1.11522,0.835661,0.767462,0.205117,0.490417,0.149272,0.777003,0.770215,0.57902,1.30903,0.184103,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,0.403887,0.273261,0.266818,0.315128,0.878738,0.26996,1.08155,1.12221,0.5687,0.212667,0.953611,0.657356,0.181004,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.59809,0.86025,0.353344,1.01535,0.48999,1.14365,0.0358067,0.329172,0.385921,2.47881,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.331322,1.73501,0.580497,1.72175,0.895708,0.153911,0.489108,0.976367,2.23719,0.637798,0.319291,1.57707,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.18312,0.445669,0.350088|tfbs_overrepresentation_jaspar=MA0003.1;1.23085,MA0004.1;0.360508,MA0006.1;1.13936,MA0007.1;0.346734,MA0009.1;0.780842,MA0014.1;0.544988,MA0017.1;0.658116,MA0019.1;0.603066,MA0024.1;0.737933,MA0025.1;1.01089,MA0027.1;2.42079,MA0028.1;2.57895,MA0029.1;0.716673,MA0030.1;0.723093,MA0031.1;0.688336,MA0038.1;0.496338,MA0040.1;0.79313,MA0041.1;0.291712,MA0042.1;0.279998,MA0043.1;0.875991,MA0046.1;0.816137,MA0048.1;0.236433,MA0050.1;0.396459,MA0051.1;0.504875,MA0052.1;0.801048,MA0055.1;0.0660514,MA0056.1;0,MA0057.1;0.471918,MA0058.1;0.752621,MA0059.1;0.28489,MA0060.1;0.8754,MA0061.1;0.504772,MA0063.1;0,MA0066.1;0.485868,MA0067.1;1.12095,MA0068.1;0.22316,MA0069.1;0.801381,MA0070.1;0.791856,MA0071.1;0.395679,MA0072.1;0.783532,MA0073.1;0.0215953,MA0074.1;0.451832,MA0076.1;3.65654,MA0077.1;0.762273,MA0078.1;0.536502,MA0081.1;0.305576,MA0083.1;0.875209,MA0084.1;1.44691,MA0087.1;0.832758,MA0088.1;1.86507,MA0089.1;0,MA0090.1;0.329158,MA0091.1;0.372635,MA0092.1;0.329444,MA0093.1;0.642324,MA0095.1;0,MA0098.1;0,MA0100.1;0.440912,MA0101.1;0.292867,MA0103.1;0.242398,MA0105.1;0.304995,MA0106.1;0.543967,MA0107.1;0.237082,MA0108.2;0.625209,MA0109.1;0,MA0111.1;0.342068,MA0113.1;0.516916,MA0114.1;0.500166,MA0115.1;0.878749,MA0116.1;0.210297,MA0117.1;0.846964,MA0119.1;0.796817,MA0122.1;0.866511,MA0124.1;1.06819,MA0125.1;0.994853,MA0130.1;0,MA0131.1;0.598671,MA0132.1;0,MA0133.1;0,MA0135.1;0.911905,MA0136.1;0.470672,MA0139.1;0.772315,MA0140.1;0.440804,MA0141.1;0.719522,MA0142.1;0.674191,MA0143.1;0.53259,MA0144.1;0.506239,MA0145.1;0.163161,MA0146.1;0.923066,MA0147.1;1.01679,MA0148.1;0.375491,MA0149.1;0.2978,MA0062.2;2.18244,MA0035.2;0.44524,MA0039.2;0.647421,MA0138.2;0.590987,MA0002.2;0.391079,MA0137.2;0.257017,MA0104.2;1.34242,MA0047.2;0.495607,MA0112.2;0.163154,MA0065.2;0.163769,MA0150.1;0.346631,MA0151.1;0,MA0152.1;0.495709,MA0153.1;0.92832,MA0154.1;0.232525,MA0155.1;0.416651,MA0156.1;0.694831,MA0157.1;0.642984,MA0158.1;0,MA0159.1;0.550545,MA0160.1;0.378276,MA0161.1;0,MA0162.1;0.27679,MA0163.1;0.439212,MA0164.1;0.471016,MA0080.2;0.669221,MA0018.2;2.09533,MA0099.2;0.584892,MA0079.2;0.432474,MA0102.2;1.49914,MA0258.1;0.473611,MA0259.1;1.56071,MA0442.1;0}} | ||
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| |||
| | |||
}} | |||
Latest revision as of 15:48, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr15:34425057..34425102,+ | p1@Pop1 |
| Mm9::chr15:8059322..8059356,+ | p1@Nup155 |
| Mm9::chr17:35378730..35378782,+ | p1@Ddx39b |
| Mm9::chr19:47165238..47165290,+ | p1@Pdcd11 |
| Mm9::chr4:129318235..129318295,- | p1@Txlna |
| Mm9::chr4:148000865..148000884,- | p1@Tardbp |
| Mm9::chr4:62069804..62069899,+ | p1@Prpf4 |
| Mm9::chr6:35127610..35127627,+ | p1@Nup205 |
| Mm9::chr8:113370670..113370698,- | p1@Sf3b3 |
| Mm9::chr8:126473101..126473187,- | p1@Nup133 |
Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data
| GO ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0005487 | nucleocytoplasmic transporter activity | 0.000749205781920186 |
| GO:0051028 | mRNA transport | 0.00407034741706452 |
| GO:0050658 | RNA transport | 0.00407034741706452 |
| GO:0051236 | establishment of RNA localization | 0.00407034741706452 |
| GO:0050657 | nucleic acid transport | 0.00407034741706452 |
| GO:0006403 | RNA localization | 0.00407034741706452 |
| GO:0005643 | nuclear pore | 0.00407034741706452 |
| GO:0065002 | intracellular protein transport across a membrane | 0.00407034741706452 |
| GO:0015931 | nucleobase, nucleoside, nucleotide and nucleic acid transport | 0.00407034741706452 |
| GO:0046930 | pore complex | 0.00407034741706452 |
| GO:0044453 | nuclear membrane part | 0.00429391984070031 |
| GO:0031965 | nuclear membrane | 0.00429391984070031 |
| GO:0044428 | nuclear part | 0.00746703842105303 |
| GO:0006913 | nucleocytoplasmic transport | 0.00746703842105303 |
| GO:0051169 | nuclear transport | 0.00746703842105303 |
| GO:0017056 | structural constituent of nuclear pore | 0.00764090439970906 |
| GO:0005635 | nuclear envelope | 0.00886461988172955 |
| GO:0005681 | spliceosome | 0.0143799144534344 |
| GO:0046540 | U4/U6 x U5 tri-snRNP complex | 0.0160755416039761 |
| GO:0008380 | RNA splicing | 0.0197360766737931 |
| GO:0051649 | establishment of cellular localization | 0.0243803738730018 |
| GO:0051641 | cellular localization | 0.0244002357987189 |
| GO:0004526 | ribonuclease P activity | 0.0248546207161951 |
| GO:0006397 | mRNA processing | 0.0248546207161951 |
| GO:0006406 | mRNA export from nucleus | 0.0248546207161951 |
| GO:0030532 | small nuclear ribonucleoprotein complex | 0.0248546207161951 |
| GO:0043123 | positive regulation of I-kappaB kinase/NF-kappaB cascade | 0.0248546207161951 |
| GO:0004549 | tRNA-specific ribonuclease activity | 0.0261400419890448 |
| GO:0016071 | mRNA metabolic process | 0.027836696568666 |
| GO:0043122 | regulation of I-kappaB kinase/NF-kappaB cascade | 0.0284511320653779 |
| GO:0006405 | RNA export from nucleus | 0.0294935597533027 |
| GO:0012505 | endomembrane system | 0.0328158581290779 |
| GO:0016891 | endoribonuclease activity, producing 5'-phosphomonoesters | 0.0369009904895174 |
| GO:0032991 | macromolecular complex | 0.0382548377726184 |
| GO:0016893 | endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters | 0.0382548377726184 |
| GO:0051168 | nuclear export | 0.0388742433313261 |
| GO:0006396 | RNA processing | 0.0398025270092647 |
| GO:0031975 | envelope | 0.0437951567695661 |
| GO:0031967 | organelle envelope | 0.0437951567695661 |
| GO:0006886 | intracellular protein transport | 0.0448957993436601 |
| GO:0016070 | RNA metabolic process | 0.0499137677017831 |
Relative expression of the co-expression cluster over median <br>Analyst:
Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>
| Ontology term | p-value | n |
|---|---|---|
| nucleate cell | 1.39e-07 | 16 |
| Ontology term | p-value | n |
|---|---|---|
| hemopoietic organ | 1.06e-09 | 29 |
| immune organ | 1.06e-09 | 29 |
| anterior region of body | 2.15e-09 | 43 |
| primordium | 2.09e-08 | 134 |
| thymus | 1.70e-07 | 23 |
| neck | 1.70e-07 | 23 |
| respiratory system epithelium | 1.70e-07 | 23 |
| hemolymphoid system gland | 1.70e-07 | 23 |
| pharyngeal epithelium | 1.70e-07 | 23 |
| thymic region | 1.70e-07 | 23 |
| pharyngeal gland | 1.70e-07 | 23 |
| entire pharyngeal arch endoderm | 1.70e-07 | 23 |
| thymus primordium | 1.70e-07 | 23 |
| early pharyngeal endoderm | 1.70e-07 | 23 |
| respiratory tract | 5.02e-07 | 41 |
| mixed endoderm/mesoderm-derived structure | 6.08e-07 | 35 |
| pharynx | 6.25e-07 | 24 |
| upper respiratory tract | 6.25e-07 | 24 |
| chordate pharynx | 6.25e-07 | 24 |
| pharyngeal arch system | 6.25e-07 | 24 |
| pharyngeal region of foregut | 6.25e-07 | 24 |
| craniocervical region | 7.77e-07 | 36 |
| segment of respiratory tract | 8.81e-07 | 27 |
TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data
Novel motifs
JASPAR motifs
| Motifs | -log10(p-value) |
|---|---|
| MA0003.1 | 1.23085 |
| MA0004.1 | 0.360508 |
| MA0006.1 | 1.13936 |
| MA0007.1 | 0.346734 |
| MA0009.1 | 0.780842 |
| MA0014.1 | 0.544988 |
| MA0017.1 | 0.658116 |
| MA0019.1 | 0.603066 |
| MA0024.1 | 0.737933 |
| MA0025.1 | 1.01089 |
| MA0027.1 | 2.42079 |
| MA0028.1 | 2.57895 |
| MA0029.1 | 0.716673 |
| MA0030.1 | 0.723093 |
| MA0031.1 | 0.688336 |
| MA0038.1 | 0.496338 |
| MA0040.1 | 0.79313 |
| MA0041.1 | 0.291712 |
| MA0042.1 | 0.279998 |
| MA0043.1 | 0.875991 |
| MA0046.1 | 0.816137 |
| MA0048.1 | 0.236433 |
| MA0050.1 | 0.396459 |
| MA0051.1 | 0.504875 |
| MA0052.1 | 0.801048 |
| MA0055.1 | 0.0660514 |
| MA0056.1 | 0 |
| MA0057.1 | 0.471918 |
| MA0058.1 | 0.752621 |
| MA0059.1 | 0.28489 |
| MA0060.1 | 0.8754 |
| MA0061.1 | 0.504772 |
| MA0063.1 | 0 |
| MA0066.1 | 0.485868 |
| MA0067.1 | 1.12095 |
| MA0068.1 | 0.22316 |
| MA0069.1 | 0.801381 |
| MA0070.1 | 0.791856 |
| MA0071.1 | 0.395679 |
| MA0072.1 | 0.783532 |
| MA0073.1 | 0.0215953 |
| MA0074.1 | 0.451832 |
| MA0076.1 | 3.65654 |
| MA0077.1 | 0.762273 |
| MA0078.1 | 0.536502 |
| MA0081.1 | 0.305576 |
| MA0083.1 | 0.875209 |
| MA0084.1 | 1.44691 |
| MA0087.1 | 0.832758 |
| MA0088.1 | 1.86507 |
| MA0089.1 | 0 |
| MA0090.1 | 0.329158 |
| MA0091.1 | 0.372635 |
| MA0092.1 | 0.329444 |
| MA0093.1 | 0.642324 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.440912 |
| MA0101.1 | 0.292867 |
| MA0103.1 | 0.242398 |
| MA0105.1 | 0.304995 |
| MA0106.1 | 0.543967 |
| MA0107.1 | 0.237082 |
| MA0108.2 | 0.625209 |
| MA0109.1 | 0 |
| MA0111.1 | 0.342068 |
| MA0113.1 | 0.516916 |
| MA0114.1 | 0.500166 |
| MA0115.1 | 0.878749 |
| MA0116.1 | 0.210297 |
| MA0117.1 | 0.846964 |
| MA0119.1 | 0.796817 |
| MA0122.1 | 0.866511 |
| MA0124.1 | 1.06819 |
| MA0125.1 | 0.994853 |
| MA0130.1 | 0 |
| MA0131.1 | 0.598671 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.911905 |
| MA0136.1 | 0.470672 |
| MA0139.1 | 0.772315 |
| MA0140.1 | 0.440804 |
| MA0141.1 | 0.719522 |
| MA0142.1 | 0.674191 |
| MA0143.1 | 0.53259 |
| MA0144.1 | 0.506239 |
| MA0145.1 | 0.163161 |
| MA0146.1 | 0.923066 |
| MA0147.1 | 1.01679 |
| MA0148.1 | 0.375491 |
| MA0149.1 | 0.2978 |
| MA0062.2 | 2.18244 |
| MA0035.2 | 0.44524 |
| MA0039.2 | 0.647421 |
| MA0138.2 | 0.590987 |
| MA0002.2 | 0.391079 |
| MA0137.2 | 0.257017 |
| MA0104.2 | 1.34242 |
| MA0047.2 | 0.495607 |
| MA0112.2 | 0.163154 |
| MA0065.2 | 0.163769 |
| MA0150.1 | 0.346631 |
| MA0151.1 | 0 |
| MA0152.1 | 0.495709 |
| MA0153.1 | 0.92832 |
| MA0154.1 | 0.232525 |
| MA0155.1 | 0.416651 |
| MA0156.1 | 0.694831 |
| MA0157.1 | 0.642984 |
| MA0158.1 | 0 |
| MA0159.1 | 0.550545 |
| MA0160.1 | 0.378276 |
| MA0161.1 | 0 |
| MA0162.1 | 0.27679 |
| MA0163.1 | 0.439212 |
| MA0164.1 | 0.471016 |
| MA0080.2 | 0.669221 |
| MA0018.2 | 2.09533 |
| MA0099.2 | 0.584892 |
| MA0079.2 | 0.432474 |
| MA0102.2 | 1.49914 |
| MA0258.1 | 0.473611 |
| MA0259.1 | 1.56071 |
| MA0442.1 | 0 |
